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How could natural selection operate so that "the good ones spread in the population" if there were no positive variants in the first place?
Sequence variants in the first intron of FTO are strongly associated with human obesity and human carriers of the risk alleles show evidence for increased appetite and food intake.
Of note, all variants in the first two groups were single and of heterozygous genotype.
In addition, although the splice site mutation in exon 8 was detected in the 'homozygous' state (similar to all nine variants downstream), we observed variants in the first exons (1 7) also in heterozygous state (Supplementary Table 10).
Common variants in the first intron of the 'fat mass and obesity associated' gene (FTO) result in an elevated body mass index (BMI) equivalent to approximately +0.4 kg/m² per risk allele.
To more directly test whether genetic variation could be co-transmitted within individual PFUs, we infected BHK cells with a 1 1 input ratio of the wild-type VSV and a monoclonal antibody-resistant (MAR) mutant at a total MOI of 20 PFU/cell to allow for extensive co-infection of cells with these two variants in the first infection cycle.
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To further define the variant MLH1 haplotype, we determined whether the novel intronic variants described in Supp. Figure S2 cosegregated with the c.-93G>A, c.-28A>G, c.-7C>T, and VILL c.1164del variants in the first-degree relative of Proband 32.
The heteroplasmy level range for these variants in the second run was 0.12 0.19%, demonstrating that these fell just outside our defined threshold for detection, but were indeed present.
While no variant in the first analysis had a P-value less than 1 × 10−6, several of the variants in the second analysis surpassed genome-wide significance (P < 5 × 10−8 from EMMAX) with the most significant SNP at rs75652600 (P = 3.12 × 10−8; OR = 4.34, 95% CI = 2.30 8.20; MAF = 4.6%).
All six variants were also detectable at comparable levels in the follow-up muscle sample taken 10 years later, although two variants in the second sample fell below the 0.2% threshold (0.17%, 0.06%).
Many current methods address this problem by using a two stage procedure where they identify a subset of variants associated with disease in a univariate fashion in the first stage, and then evaluate interactions only within this smaller set of variants in the second stage [ 2].
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